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9teh

PhiC31 excisive synapse; attL x attL with an integraseS12A-RDF protein fusion

Method: ELECTRON MICROSCOPY D_max: 243.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9teh
deposition_date	2025-11-25
title	PhiC31 excisive synapse; attL x attL with an integraseS12A-RDF protein fusion
keywords	Serine integrase, Recombinase, Site-specific recombination, RDF, DNA, RECOMBINATION; RECOMBINATION
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	70.82 Å
rg_electron	70.87 Å
i0	2520740000.00
molecular_weight	372060.0 kDa
excluded_volume	444030 Å³
envelope_volume	775200 Å³
shell_volume	95737 Å³
envelope_diameter	234.5 Å
shell_rg	67.79 Å
envelope_rg	66.48 Å
shape_rg	70.92 Å
total_rg	70.68 Å
total_atoms	25890
n_residues	2944
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	243.7 Å
rg_real	70.79 Å
rg_real_error	2.67 Å
i0_real	2.5210e+09
i0_real_error	5.8400e+07
rg_reciprocal	70.75 Å
i0_reciprocal	2520000000.0000
total_estimate	0.8571
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	99.7 Å
skewness	0.153
kurtosis	-0.506
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.0003
highest_alpha	53910000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.602

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Integrase
formula_weight	69566.4 kDa
mutation	S12A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	25890

MGSSHHHHHHSSGLVPRGSHMDTYAGAYDRQARERENSSAASPATQRSANEDKAADLQREVERDGGRFRFVGHFSEAPGTSAFGTAERPEFERILNECRAGRLNMIIVYDVSRFSRLKVMDAIPIVSELLALGVTIVSTQEGVFRQGNVMDLIHLIMRLDASHKESSLKSAKILDTKNLQRELGGYVGGKAPYGFELVSETKEITRNGRMVNVVINKLAHSTTPLTGPFEFEPDVIRWWWREIKTHKHLPFKPGSQAAIHPGSITGLCKRMDADAVPTRGETIGKKTASSAWDPATVMRILRDPRIAGFAAEVIYKKKPDGTPTTKIEGYRIQRDPITLRPVELDCGPIIEPAEWYELQAWLDGRGRGKGLSRGQAILSAMDKLYCECGAVMTSKRGEESIKDSYRCRRRKVVDPSAPGQHEGTCNVSMAALDKFVAERIFNKIRHAEGDEETLALLWEAARRFGKLTEAPEKSGERANLVAERADALNALEELYEDRAAGAYDGPVGRKHFRKQQAALTLRQQGAEERLAELEAAEAPKLPLDQWFPEDADADPTGPKSWWGRASVDDKRVFVGLFVDKIVVTKSTTGRGQGTPIEKRASITWAKPPTDDDEDDAQDGTEDVAATS

Source

organism	Lomovskayavirus C31
ncbi_taxonomy_id	10719
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	DNA (55-MER)
formula_weight	18701.9 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	E,G

AGCCGCGGTGCGGGTGCCAGGGCGTGCCCTTGAGTTCTCTCAGTTGGGGGCGTAGGGTCG

Entity 3 polymer

description	DNA (55-MER)
formula_weight	18293.7 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	F,H

CGACCCTACGCCCCCAACTGAGAGAACTCAAGGGCACGCCCTGGCACCCGCACCGCGGCT

Entity 4 polymer

description	Recombination directionality factor
formula_weight	30669.3 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	I,J,K,L

MSYYHHHHHHDYDIPTTENLYFQGAMAMAKRSIWAGDEDNKPKKRETYADDTVGRFHSGYSETNERGKVVPVALDKWRISTGEQSVADAVAQLFGGTPVENEESTSENFIDVFTDRPKVPVIIEADGIHWDMKLWLNGKLKHHCDGFDFVSHADEEMIGQPCGCPKLFDERKAAAKEYDAPNPAITVTFTLADDPELGRFKFQTGSWTLFKVLHEAEDDVERVGKGGAVLANLELELVEYTPKRGPMRNKLVSYYKPTITVLKSYNDAIAD

Source

organism	Lomovskayavirus C31
ncbi_taxonomy_id	10719
host_organism	Escherichia coli BL21(DE3)

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	7.23 Å
resolution_method	—
num_particles	17432

fit	/app/data/saxs_computation/te/9teh/9teh.fit
pddf	/app/data/pr_computation/te/9teh/9teh.pr.out
profile	/app/data/saxs_computation/te/9teh/9teh.dat

PhiC31 excisive synapse; attL x attL with an integraseS12A-RDF protein fusion

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)